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Faith Okamoto

Code unto others as you would have them code unto you

👋🏽 My CV is available. 👋🏽

Documenting options

What choices do I have?
By Faith Okamoto
Posted on May 3, 2025

I recently identified a problem with vg filter’s --tsv-out option. Namely, that a command to write “a tsv of the given fields” didn’t document which fields were possible. This command is quite important to running QC on our GAM and GAMP alignment files. Those files aren’t human-readable, so if a... [Read More]
Tags:
- documentation
- parameters
Format your code

April 2025
By Faith Okamoto
Posted on April 26, 2025

I’m running out of time for this month’s published-code-critique. Luckily, Nature’s front page had this gem: a paper literally referring back to the days of Mendel1! [Read More]
Tags:
- published-code-critique
- style
Directory READMEs

From the list of "things I wish other people did"
By Faith Okamoto
Posted on April 19, 2025

I’ve mentioned that I make a README as the first file in any new project directory. Here, I’ll detail what goes in this README. [Read More]
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Magic numbers in plotting

Abracadabra, make a graph!
By Faith Okamoto
Posted on April 5, 2025

I’ve just started a class on making scientific plots so I’ll cover a common phenomenon: magic numbers. [Read More]
Tags:
- style
- plots
A pretty good README

March 2025
By Faith Okamoto
Posted on March 20, 2025

Figured I could do with some praise, and luckily enough, the first manuscript in Bioinformatics’s “Advance articles” section fit the bill. [Read More]
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